i like this post (click again to cancel)
i dont like this post (click again to cancel) remove favorite mark from this question (click again to restore mark)

I have studied several protein-protein interactions and often binding will result in very large proton shifts, I know alot of people will blame this on packing against or proximity to an aromatic ring or something of that nature, recently ive come across a few paticularly large shifts say 1.5-2 ppm and its been sugested these are too big for aromatic shifts and must be from the formation of a hydrogen bond.

does anyone know any good papers/ databases where the max shift you can expect from aromatic effects have been examined?

asked Jul 16 '10 at 15:16

TomgA20's gravatar image


updated Jul 17 '10 at 10:37

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

One Answer:
i like this answer (click again to cancel)
i dont like this answer (click again to cancel)

If you set paramagnetic structures aside, there are up to +2/-4 ppm variations in the chemical shifts of aromatic residues (Phe, Tyr, Trp) from the average values. Variation in non-aromatic residues is not smaller, so it probably has more to do with the local environment rather than the nature of the residue itself.

The chemical shift variation is far greater (may be hundreds of ppm) in paramagnetic species due to contact and pseudocontact shifts.

BMRB - Biological Magnetic Resonance Data Bank has the most comprehensive collection of such data, including histograms of chemical shifts in each aminoacid. Their "outlier" tables list chemical shifts of each atom and give link to the source data.

This page has links to histograms assembled from full set of protein data and this one has data from diamagnetic proteins only.

This paper (by Nian E. Zhou, Bing Yan Zhu, Brian D. Sykes and Robert S. Hodges) has a discussion of amide chemical shift in relation to the length of the hydrogen bond on an amphipathic alpha-helical peptide which has a curved geometry (bent towards the hydrophobic part). Amide chemical shift changed by a maximum of +/- 0.7 ppm compared to the random coil value, where increase corresponded to the hydrophobic lobe and decrease - to hydrophilic lobe, so the shorter is the hydrogen bond, the higher is chemical shift of the amide residue.


answered Jul 17 '10 at 10:11

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

updated Jul 18 '10 at 10:12

Your answer
Please start posting your answer anonymously - your answer will be saved within the current session and published after you log in or create a new account. Please try to give a good answer, for discussions, please use comments and please do remember to vote (login to vote)
toggle preview

powered by CNPROG